The Indian SARS-CoV-2 Consortium on Geno

Feb 02, 2022

Q What is the context ?

A The Indian SARS-CoV-2 Consortium on Genomics (INSACOG) has sequenced about 1,00,000 samples.

Q What is INSACOG?

INSACOG is a consortium of 10 labs and 18 satellite labs across India tasked with scanning COVID samples from patients and finding the variants that has led to spike in transmission.
The institutes involved include the laboratories of the Department of Biotechnology, Council of Scientific and Industrial Research, Indian Council of Medical Research, and the Health Ministry.
Its work began in January 2020, by sequencing all samples with a history of travel from the U.K. and a proportion of positive samples in the community.

Q What are the tasks of INSACOG ?

The NCDC is tasked with coordinating collections of samples from the States as well as correlating disease with certain mutations.
It is mainly involved in genomic sequencing which is done by isolating the genetic material of the coronavirus samples.
It is also tasked with tracking certain combinations of mutations that become more widespread in India.

Q What has it found so far?

The INSACOG sequenced about 1,00,000 samples as of early December 2021 when this data was last made publicly available.
The bulk of its effort has been focussed on identifying international ‘variants of concern’ (VoC) that are marked out by the WHO as being particularly infectious or pathogenic.
International travellers who arrive in India and test positive are the ones whose samples usually get sent to INSACOG for determining the genomic variant.

Q Why is genome sequencing useful?

Understanding mutations: The purpose of genome sequencing is to understand the role of certain mutations in increasing the virus’s infectivity.
Immune response: Some mutations have also been linked to immune escape, or the virus’s ability to evade antibodies, and this has consequences for vaccines.
Effectiveness of vaccines: Labs across the world, including many in India, have been studying if the vaccines developed so far are effective against such mutant strains of the virus.
Evolution of viruses: Studies such as this have shown that Omicron, for instance, has evolved to evade antibodies much better than the Alpha or Delta variant. This prompted the push towards booster doses.

Q How is it done?

Genomic sequencing is done by isolating the genetic material (RNA) of the coronavirus samples.
RNA consists of millions of nucleotide bases and genomic sequencing is about identifying and comparing the sequence in a given sample to a reference sample.
Changes in the sequence are clues to mutations that show that the virus may have undergone distinct changes at some key locations.
There are several approaches to genome sequencing whole genome sequencing, next-generation sequencing that have different advantages.
It has now evolved to a stage where large sequencers can process even thousands of samples simultaneously.

Q What are various challenges that INSACOG faces ?

Geographical variations: Given that COVID-19 is spreading, mutating and showing geographical variations, the original aim of the group was to sequence at least 5% of COVID-19 samples.
Shortage of funds: But only 1% has been achieved yet, primarily due to a shortage of funds, insufficient reagents and tools necessary to rapidly scale up.
Red-tapism: The INSACOG, in spite of being peopled by expert scientists, is ultimately within the Central government’s communication structure.
Infrastructure lacunae: Not all INSACOG labs have the same quality of equipment and manpower and therefore a surge or spike in some cities can mean difficulties in processing.